/*=========================================================================
 *
 *  Copyright Insight Software Consortium
 *
 *  Licensed under the Apache License, Version 2.0 (the "License");
 *  you may not use this file except in compliance with the License.
 *  You may obtain a copy of the License at
 *
 *         http://www.apache.org/licenses/LICENSE-2.0.txt
 *
 *  Unless required by applicable law or agreed to in writing, software
 *  distributed under the License is distributed on an "AS IS" BASIS,
 *  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 *  See the License for the specific language governing permissions and
 *  limitations under the License.
 *
 *=========================================================================*/

//  Software Guide : BeginLatex
//
//  This example illustrates how to use the WarpImageFilter and a
//  deformation field for resampling an image. This is typically done
//  as the last step of a deformable registration algorithm.
//
//  \index{itk::WarpImageFilter}
//
//  Software Guide : EndLatex


#include "itkImage.h"
#include "itkImageFileReader.h"
#include "itkImageFileWriter.h"


// Software Guide : BeginCodeSnippet
#include "itkWarpImageFilter.h"
// Software Guide : EndCodeSnippet


int main( int argc, char * argv[] )
{
  if( argc < 4 )
    {
    std::cerr << "Usage: " << std::endl;
    std::cerr << argv[0] << "  inputImageFile  inputDisplacementField  outputImageFile" << std::endl;
    return EXIT_FAILURE;
    }

  const     unsigned int   Dimension = 2;

  // Software Guide : BeginLatex
  // The deformation field is represented as an image of vector pixel types. The
  // dimension of the vectors is the same as the dimension of the input image.
  // Each vector in the deformation field represents the distance between a
  // geometric point in the input space and a point in the output space such that:
  // \begin{equation}
  // p_{in} = p_{out} + distance
  // \end{equation}
  // Software Guide : EndLatex
  // Software Guide : BeginCodeSnippet
  typedef   float                                         VectorComponentType;
  typedef   itk::Vector< VectorComponentType, Dimension > VectorPixelType;
  typedef   itk::Image< VectorPixelType,  Dimension >     DisplacementFieldType;

  typedef   unsigned char                         PixelType;
  typedef   itk::Image< PixelType,  Dimension >   ImageType;
  // Software Guide : EndCodeSnippet


  typedef   itk::ImageFileReader< ImageType >  ReaderType;
  typedef   itk::ImageFileWriter< ImageType >  WriterType;

  // Software Guide : BeginLatex
  // The field is read from a file, through a reader instantiated over the
  // vector pixel types.
  // Software Guide : EndLatex
  // Software Guide : BeginCodeSnippet
  typedef   itk::ImageFileReader< DisplacementFieldType >  FieldReaderType;
  // Software Guide : EndCodeSnippet

  ReaderType::Pointer reader = ReaderType::New();
  WriterType::Pointer writer = WriterType::New();

  reader->SetFileName( argv[1] );
  writer->SetFileName( argv[3] );

  // Software Guide : BeginCodeSnippet
  FieldReaderType::Pointer fieldReader = FieldReaderType::New();
  fieldReader->SetFileName( argv[2] );
  fieldReader->Update();

  DisplacementFieldType::ConstPointer deformationField = fieldReader->GetOutput();
  // Software Guide : EndCodeSnippet

  // Software Guide : BeginLatex
  // The \doxygen{WarpImageFilter} is templated over the input image type, output
  // image type and the deformation field type.
  // Software Guide : EndLatex
  // Software Guide : BeginCodeSnippet
  typedef itk::WarpImageFilter< ImageType,
                                ImageType,
                                DisplacementFieldType  >  FilterType;

  FilterType::Pointer filter = FilterType::New();
  // Software Guide : EndCodeSnippet

  // Software Guide : BeginLatex
  // Typically the mapped position does not correspond to an integer pixel position
  // in the input image. Interpolation via an image function is used to compute
  // values at non-integer positions.
  // This is done via the \code{SetInterpolator()} method.
  // \index{itk::Warp\-Image\-Filter!SetInterpolator()}
  // Software Guide : EndLatex
  // Software Guide : BeginCodeSnippet
  typedef itk::LinearInterpolateImageFunction<
                       ImageType, double >  InterpolatorType;

  InterpolatorType::Pointer interpolator = InterpolatorType::New();

  filter->SetInterpolator( interpolator );
  // Software Guide : EndCodeSnippet

  // SoftwareGuide : BeginLatex
  // The output image spacing and origin may be set via SetOutputSpacing(),
  // SetOutputOrigin(). This is taken from the deformation field.
  // Software Guide : EndLatex
  // Software Guide : BeginCodeSnippet
  filter->SetOutputSpacing( deformationField->GetSpacing() );
  filter->SetOutputOrigin(  deformationField->GetOrigin() );
  filter->SetOutputDirection(  deformationField->GetDirection() );

  filter->SetDisplacementField( deformationField );
  // Software Guide : EndCodeSnippet

  filter->SetInput( reader->GetOutput() );
  writer->SetInput( filter->GetOutput() );

  try
    {
    writer->Update();
    }
  catch( itk::ExceptionObject & excp )
    {
    std::cerr << "Exception thrown " << std::endl;
    std::cerr << excp << std::endl;
    }

  return EXIT_SUCCESS;

}
